You know,I'm tempted to sit back and see what other people have to say about the themes of the book, but I don't think it's any secret that the book is, on one level, all about pitting good, old-fashioned Star Trek multiculturalism against militant fundamentalism. And when writing the book, I at least tried to make it clear that I was criticizing fundamentalism in general, not any specific religion.
And BrentMC, don't worry about bringing it up. I kinda figured that the religious elements in the book would provoke a bit of discussion at some point. (I'm actually surprised that it took this long!)